Sequence features of E. coli mRNAs affect their degradation.

Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect it...

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Autores principales:	Gal Lenz, Adi Doron-Faigenboim, Eliora Z Ron, Tamir Tuller, Uri Gophna
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6ddfdddba2e84971a66980245631def0
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id	oai:doaj.org-article:6ddfdddba2e84971a66980245631def0
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spelling	oai:doaj.org-article:6ddfdddba2e84971a66980245631def02021-11-18T07:32:49ZSequence features of E. coli mRNAs affect their degradation.1932-620310.1371/journal.pone.0028544https://doaj.org/article/6ddfdddba2e84971a66980245631def02011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22163312/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect its stability are yet to be elucidated. We calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI) and folding energy. Each of these properties were then correlated with the experimental transcript half life measured for each transcript and detected significant correlations. A sliding window analysis identified the regions that displayed the maximal signal. The correlation between transcript half life and both G+C content and folding energy was strongest at the 5' termini of the mRNAs. Partial correlations showed that each of the parameters contributes separately to mRNA half life. Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes.Gal LenzAdi Doron-FaigenboimEliora Z RonTamir TullerUri GophnaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 12, p e28544 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gal Lenz Adi Doron-Faigenboim Eliora Z Ron Tamir Tuller Uri Gophna Sequence features of E. coli mRNAs affect their degradation.
description	Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect its stability are yet to be elucidated. We calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI) and folding energy. Each of these properties were then correlated with the experimental transcript half life measured for each transcript and detected significant correlations. A sliding window analysis identified the regions that displayed the maximal signal. The correlation between transcript half life and both G+C content and folding energy was strongest at the 5' termini of the mRNAs. Partial correlations showed that each of the parameters contributes separately to mRNA half life. Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes.
format	article
author	Gal Lenz Adi Doron-Faigenboim Eliora Z Ron Tamir Tuller Uri Gophna
author_facet	Gal Lenz Adi Doron-Faigenboim Eliora Z Ron Tamir Tuller Uri Gophna
author_sort	Gal Lenz
title	Sequence features of E. coli mRNAs affect their degradation.
title_short	Sequence features of E. coli mRNAs affect their degradation.
title_full	Sequence features of E. coli mRNAs affect their degradation.
title_fullStr	Sequence features of E. coli mRNAs affect their degradation.
title_full_unstemmed	Sequence features of E. coli mRNAs affect their degradation.
title_sort	sequence features of e. coli mrnas affect their degradation.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/6ddfdddba2e84971a66980245631def0
work_keys_str_mv	AT gallenz sequencefeaturesofecolimrnasaffecttheirdegradation AT adidoronfaigenboim sequencefeaturesofecolimrnasaffecttheirdegradation AT eliorazron sequencefeaturesofecolimrnasaffecttheirdegradation AT tamirtuller sequencefeaturesofecolimrnasaffecttheirdegradation AT urigophna sequencefeaturesofecolimrnasaffecttheirdegradation
_version_	1718423291254800384

Sequence features of E. coli mRNAs affect their degradation.

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